I would like to suggest a way of letting users customize project workflow via the usage of projects.
For some hobby programs, I've found that using multiple libraries with all their code under the same project renders the project... noisy. Make that extremely noisy.
I'm not sure how this applies to other IDEs other than Visual Studio, but my suggestion would be having the possibility of keeping JUCE within its own project, and having my application's project separate from it if desired. (And having the ability to add other ones, too!)
Your workflow may differ, but I find this inconvenient.
The image I've uploaded is a mock-up example of the possible usefulness; a solution "using" JUCE and VFLib together, in separate projects. VFLib would obviously depend on JUCE, and MyProject would simply need to depend on VFLib.
[Visual Studio 2012] [Xcode 6.4]